RetrogeneDB ID: retro_mdom_962

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:38795912..38796592(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: ENDOU
• Ensembl ID: ENSMODG00000009733
• Aliases: None
• Description: endonuclease, polyU-specific [Source:HGNC Symbol;Acc:14369]

Sequence

>retro_mdom_962
CTCTACAGCTGCGTAAATGGAGAACTCTTCTCCAAACTAGCGTATGCTGCATTCATCAGTCTACTCAATAACTACCACCG
GCTAACAGGCCAGGGGGGACACTTCCATTCTCAGCACCTTGAGGAACAGGACACTTTTCTTCCAGAGATAATGAAGTCAA
TAGTCATGAAGGAACTCAATGGTTTCCTCCATCAAAAAAACACATACAGCTCCGAGCAAGAATTTGTCAGTGACAGGAAG
AAGATGTGGATGGGGTTGTATTCCCGGGGCCAGGATGAGGGTGACTCCAGTGGCTTTGAACACGTTTTCTCTGGTGAAGT
GAAAAAGGGAAAAGTGTCAGATTCCATGGCTGGATCCACTTCTACCTGCAGGAGGAGGGTCTGGTCGACTATTACAGCCA
CAACTATGACGGGCCGTGGGACTCGTATCCTGATGTGCTAGGAATGCAATTCAACTGGGATGGCAACTTCAAAGAAGTGG
GATCGACGTTCATGGGCAGTCCGGAGTGTGAATTTGCCCTCTCTTCCTTGTGCTTCATCAGCAGACCTGGCGGTGTGTGT
CATTTGAGCCCCGGGGTGGGGGGGCACCCCCTGGCTATCCAAATCTAGACCTGGGCCACAGTGACCTATGGAAATGGCAA
GAAGTACTTTGCCAAAGCCTATATAGTATCTTCTACGGAT

Alignment

ORF - retro_mdom_962 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.04 %
• Parental protein coverage: 55.5 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LYSYVNEELFSKPTYAAFISLLNNYHRVTGQGEHFSSQQLEEQDTFLREIMKTAVMKELYGFLHQKNRYS
          LYS.VN.ELFSK..YAAFISLLNNYHR.TGQG.HF.SQ.LEEQDTFL.EIMK..VMKEL.GFLHQKN.YS
Retrocopy LYSCVNGELFSKLAYAAFISLLNNYHRLTGQGGHFHSQHLEEQDTFLPEIMKSIVMKELNGFLHQKNTYS

Parental  SEQEFVSDLKKMWFGLYSRGHDEGDSSGFEHVFSGEVKKGKVSG-FHNWIRFYLQEKEGLVDYYSHNYDG
          SEQEFVSD.KKMW.GLYSRG.DEGDSSGFEHVFSGEVKKGKVS..FH.WI.FYLQE.EGLVDYYSHNYDG
Retrocopy SEQEFVSDRKKMWMGLYSRGQDEGDSSGFEHVFSGEVKKGKVSD<FHGWIHFYLQE-EGLVDYYSHNYDG

Parental  PWDSYPDVLGMQFNWDGYFKEVGSAFIGSSPEFEFALYSLCFISRPGGVCHLS--LGGYPLAIKTYTWDK
          PWDSYPDVLGMQFNWDG.FKEVGS.F.G.SPE.EFAL.SLCFISRPGGVCHLS...GG.PLAI...TW..
Retrocopy PWDSYPDVLGMQFNWDGNFKEVGSTFMG-SPECEFALSSLCFISRPGGVCHLSPGVGGHPLAIQI*TWAT

Parental  VTYGNGKKYIATAYIVSSTN
          VTYGNGKKY.A.AYIVSST.
Retrocopy VTYGNGKKYFAKAYIVSSTD

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.00 RPM	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_962 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_962 was not experimentally validated.

Homology

Retrocopy orthology:

Monodelphis domestica does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000009733	2 retrocopies	retro_mdom_1285, retro_mdom_962 ,